Are you printing in draft mode? I had a similar problem with faint/ barely visible lines when I set my printer properties too low. I reset my propoerties to fine and fold and cut lines became very clear.
ok unfortunately youll need to reprint when youre in pepakura designer theres a symbol/button on the menu bar it has a red rectangle with the numbers 1,2,3 click on it when the little screen pops up click edge id configuration so there is a little check mark beside it. alo on this screen you can adjust the number size this makes it easier with the assembly because you can see the numbers better. ALSO this should be in the pepakura and cardboard armour forums not the molded armour forums